Judith Klein-Seetharaman

Judith Klein-Seetharaman

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Judith Klein-Seetharaman

Judith Klein-Seetharaman

Publications by authors named "Judith Klein-Seetharaman"

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Structural and Functional Consequences of the Weak Binding of Chlorin e6 to Bovine Rhodopsin.

Photochem Photobiol 2018 Dec 24. Epub 2018 Dec 24.

Biomedical Sciences Division, Warwick Medical School, University of Warwick, Coventry, UK.

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http://doi.wiley.com/10.1111/php.13074
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http://dx.doi.org/10.1111/php.13074DOI Listing
December 2018

Characterization of Denatured States and Reversible Unfolding of Sensory Rhodopsin II.

J Mol Biol 2018 Oct 9;430(21):4068-4086. Epub 2018 Aug 9.

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2018.07.031DOI Listing
October 2018

Structural characterization of cardiolipin-driven activation of cytochrome c into a peroxidase and membrane perturbation.

Biochim Biophys Acta Biomembr 2018 May 6;1860(5):1057-1068. Epub 2018 Jan 6.

Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry CV4 7AL, UK. Electronic address:

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http://dx.doi.org/10.1016/j.bbamem.2018.01.009DOI Listing
May 2018

Chlorophyll-Derivative Modulation of Rhodopsin Signaling Properties through Evolutionarily Conserved Interaction Pathways.

Front Mol Biosci 2017 12;4:85. Epub 2017 Dec 12.

Warwick Medical School, University of Warwick, Coventry, United Kingdom.

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http://dx.doi.org/10.3389/fmolb.2017.00085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5733091PMC
December 2017

Structure and dynamics of the insulin receptor: implications for receptor activation and drug discovery.

Drug Discov Today 2017 07 3;22(7):1092-1102. Epub 2017 May 3.

Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA; Division of Metabolic and Vascular Health & Systems, Medical School, University of Warwick, Coventry CV4 7AL, UK. Electronic address:

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http://dx.doi.org/10.1016/j.drudis.2017.04.011DOI Listing
July 2017

Multitask Matrix Completion for Learning Protein Interactions Across Diseases.

J Comput Biol 2017 Jun 27;24(6):501-514. Epub 2017 Jan 27.

3 Metabolic & Vascular Health, Warwick Medical School, University of Warwick , Coventry, United Kingdom .

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http://dx.doi.org/10.1089/cmb.2016.0201DOI Listing
June 2017

Known unknowns of cardiolipin signaling: The best is yet to come.

Biochim Biophys Acta Mol Cell Biol Lipids 2017 Jan 4;1862(1):8-24. Epub 2016 Aug 4.

Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Critical Care Medicine, Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15260, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bbalip.2016.08.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5323096PMC
January 2017

Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors.

Sci Rep 2016 11 16;6:37290. Epub 2016 Nov 16.

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.

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http://www.nature.com/articles/srep37290
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http://dx.doi.org/10.1038/srep37290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5110974PMC
November 2016

Refining literature curated protein interactions using expert opinions.

Pac Symp Biocomput 2015 :318-29

Department of Computer Engineering, Bilkent University, Cankaya, Ankara, Turkey.

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April 2016

Cardiolipin Interactions with Proteins.

Biophys J 2015 Sep 20;109(6):1282-94. Epub 2015 Aug 20.

Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry, United Kingdom; Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2015.07.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576322PMC
September 2015

Mitochondrial NM23-H4/NDPK-D: a bifunctional nanoswitch for bioenergetics and lipid signaling.

Naunyn Schmiedebergs Arch Pharmacol 2015 Feb 18;388(2):271-8. Epub 2014 Sep 18.

Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France,

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http://dx.doi.org/10.1007/s00210-014-1047-4DOI Listing
February 2015

Comparing human-Salmonella with plant-Salmonella protein-protein interaction predictions.

Front Microbiol 2015 28;6:45. Epub 2015 Jan 28.

Klein-Seetharaman Laboratory, Division of Metabolic and Vascular Health, Warwick Medical School, University of Warwick , Coventry, UK.

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http://dx.doi.org/10.3389/fmicb.2015.00045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309195PMC
February 2015

Techniques for transferring host-pathogen protein interactions knowledge to new tasks.

Front Microbiol 2015 2;6:36. Epub 2015 Feb 2.

Metabolic and Vascular Health, Warwick Medical School, University of Warwick Coventry, UK.

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http://dx.doi.org/10.3389/fmicb.2015.00036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313693PMC
February 2015

Molecular speciation and dynamics of oxidized triacylglycerols in lipid droplets: Mass spectrometry and coarse-grained simulations.

Free Radic Biol Med 2014 Nov 10;76:53-60. Epub 2014 Aug 10.

Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15219, USA. Electronic address:

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http://dx.doi.org/10.1016/j.freeradbiomed.2014.07.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4276254PMC
November 2014

Differential dynamics of extracellular and cytoplasmic domains in denatured States of rhodopsin.

Biochemistry 2014 Nov 10;53(46):7160-9. Epub 2014 Nov 10.

Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.

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http://dx.doi.org/10.1021/bi401557eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245987PMC
November 2014

Structural re-arrangement and peroxidase activation of cytochrome c by anionic analogues of vitamin E, tocopherol succinate and tocopherol phosphate.

J Biol Chem 2014 Nov 2;289(47):32488-98. Epub 2014 Oct 2.

From the Center for Free Radical and Antioxidant Health, the Departments of Environmental and Occupational Health, Pharmacology and Chemical Biology, Radiation Oncology, and Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260.

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http://dx.doi.org/10.1074/jbc.M114.601377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239604PMC
November 2014

Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology.

BMC Biophys 2014 5;7. Epub 2014 Aug 5.

Graduate Program in Molecular Biophysics and Structural Biology, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, PA 15260, USA ; Department of Structural Biology, University of Pittsburgh, Pittsburgh, USA ; Presently at: Department of Biomedicine and Systems Biology, Division of Metabolic and Vascular Health, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK.

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http://dx.doi.org/10.1186/2046-1682-7-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4134111PMC
August 2014

A mitochondrial pathway for biosynthesis of lipid mediators.

Nat Chem 2014 Jun 20;6(6):542-52. Epub 2014 Apr 20.

1] Center for Free Radical and Antioxidant Health University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA [2] Department of Environmental Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.

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http://dx.doi.org/10.1038/nchem.1924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201180PMC
June 2014

Retinal proteins as model systems for membrane protein folding.

Biochim Biophys Acta 2014 May 12;1837(5):656-63. Epub 2013 Dec 12.

Division of Metabolic and Vascular Health, Warwick Medical School, University of Warwick, Coventry, UK. Electronic address:

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http://dx.doi.org/10.1016/j.bbabio.2013.11.021DOI Listing
May 2014

X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes.

Chem Phys Lipids 2014 Feb 28;178:1-10. Epub 2013 Dec 28.

Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States. Electronic address:

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http://dx.doi.org/10.1016/j.chemphyslip.2013.12.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026202PMC
February 2014

Characterization of the simultaneous decay kinetics of metarhodopsin states II and III in rhodopsin by solution-state NMR spectroscopy.

Angew Chem Int Ed Engl 2014 Feb 6;53(8):2078-84. Epub 2014 Feb 6.

Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany).

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http://dx.doi.org/10.1002/anie.201309581DOI Listing
February 2014

Determining confidence of predicted interactions between HIV-1 and human proteins using conformal method.

Pac Symp Biocomput 2012 :311-22

Computer Learning Research Centre, Royal Holloway University of London, London, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249613PMC
December 2013

Multitask learning for host-pathogen protein interactions.

Bioinformatics 2013 Jul;29(13):i217-26

Language Technologies Institute, School of Computer Science, Carnegie Mellon University, 5000 Forbes Ave, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694681PMC
July 2013

Identification of motions in membrane proteins by elastic network models and their experimental validation.

Methods Mol Biol 2012 ;914:285-317

Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1007/978-1-62703-023-6_17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801040PMC
January 2013

In support of the BMRB.

Nat Struct Mol Biol 2012 Sep;19(9):854-60

University of Wisconsin-Madison, Madison, Wisconsin, USA.

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http://dx.doi.org/10.1038/nsmb.2371DOI Listing
September 2012

Techniques to cope with missing data in host-pathogen protein interaction prediction.

Bioinformatics 2012 Sep;28(18):i466-i472

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436802PMC
September 2012

BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference.

Nucleic Acids Res 2012 Jul 11;40(Web Server issue):W147-51. Epub 2012 Jun 11.

Structural Bioinformatics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB), 08003 Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1093/nar/gks553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394316PMC
July 2012

A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors.

BMC Biophys 2012 Jun 29;5:13. Epub 2012 Jun 29.

Computer Science Department, Carnegie Mellon University, Gates Hillman Center, 5000 Forbes Avenue, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1186/2046-1682-5-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3478154PMC
June 2012

Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes.

Chem Biodivers 2012 May;9(5):991-1018

Forschungszentrum Jülich, Institute of Complex Systems (ICS-5), D-52425 Jülich, Germany.

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http://dx.doi.org/10.1002/cbdv.201100392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3407687PMC
May 2012

Isotope labeling in insect cells.

Methods Mol Biol 2012 ;831:37-54

Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Frankfurt am Main, Germany.

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http://link.springer.com/10.1007/978-1-61779-480-3_3
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http://dx.doi.org/10.1007/978-1-61779-480-3_3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249615PMC
April 2012

Isotope labeling in mammalian cells.

Methods Mol Biol 2012 ;831:55-69

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1007/978-1-61779-480-3_4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3263381PMC
April 2012

The cytoplasmic rhodopsin-protein interface: potential for drug discovery.

Curr Drug Targets 2012 Jan;13(1):3-14

Department of Structural Biology, Biomedical Science Tower 3, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3275648PMC
January 2012

The current Salmonella-host interactome.

Proteomics Clin Appl 2012 Jan 27;6(1-2):117-33. Epub 2011 Dec 27.

Forschungszentrum Jülich, Institute of Complex Systems, Jülich, Germany.

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http://doi.wiley.com/10.1002/prca.201100083
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http://dx.doi.org/10.1002/prca.201100083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312997PMC
January 2012

Virus interactions with human signal transduction pathways.

Int J Comput Biol Drug Des 2011 17;4(1):83-105. Epub 2011 Feb 17.

Departments of Biomedical Informatics, Psychiatry, and Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.

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http://dx.doi.org/10.1504/IJCBDD.2011.038658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3407688PMC
May 2011

Discovering pathways by orienting edges in protein interaction networks.

Nucleic Acids Res 2011 Mar 24;39(4):e22. Epub 2010 Nov 24.

Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1093/nar/gkq1207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045580PMC
March 2011

The enzymatic oxidation of graphene oxide.

ACS Nano 2011 Mar 23;5(3):2098-108. Epub 2011 Feb 23.

Department of Chemistry, University of Pittburgh, Pittsburgh, PA 15260, USA.

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http://dx.doi.org/10.1021/nn103265hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062704PMC
March 2011

Allosteric Modulation of G Protein Coupled Receptors by Cytoplasmic, Transmembrane and Extracellular Ligands.

Pharmaceuticals (Basel) 2010 Oct;3(10):3324-3342

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.

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http://dx.doi.org/10.3390/ph3103324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760430PMC
October 2010

Ligand-independent antiapoptotic function of estrogen receptor-beta in lung cancer cells.

Mol Endocrinol 2010 Sep 21;24(9):1737-47. Epub 2010 Jul 21.

Division of Endocrinology and Metabolism, University of Pittsburgh, E1115 Starzl Biomedical Science Tower, 200 Lothrop Street, Pittsburgh, PA 15261, USA.

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http://dx.doi.org/10.1210/me.2010-0125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940472PMC
September 2010

Characterization of membrane protein non-native states. 1. Extent of unfolding and aggregation of rhodopsin in the presence of chemical denaturants.

Biochemistry 2010 Aug;49(30):6317-28

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.

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http://dx.doi.org/10.1021/bi100338eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243665PMC
August 2010

Characterization of membrane protein non-native states. 2. The SDS-unfolded states of rhodopsin.

Biochemistry 2010 Aug;49(30):6329-40

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.

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http://dx.doi.org/10.1021/bi100339xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243666PMC
August 2010

Flexibility of the cytoplasmic domain of the phototaxis transducer II from Natronomonas pharaonis.

J Biophys 2008 16;2008:267912. Epub 2008 Oct 16.

Institute for Structural Biology (IBI-2), Research Center Jülich, 52425 Jülich, Germany.

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http://dx.doi.org/10.1155/2008/267912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2809331PMC
June 2010

Carbon nanotubes degraded by neutrophil myeloperoxidase induce less pulmonary inflammation.

Nat Nanotechnol 2010 May 4;5(5):354-9. Epub 2010 Apr 4.

Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.1038/nnano.2010.44DOI Listing
May 2010

NMR-based screening of membrane protein ligands.

Chem Biol Drug Des 2010 Mar;75(3):237-56

Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA15260, USA.

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http://dx.doi.org/10.1111/j.1747-0285.2009.00940.xDOI Listing
March 2010

The importance of valine 114 in ligand binding in beta(2)-adrenergic receptor.

Protein Sci 2010 Jan;19(1):85-93

Department of Oral Biology, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0W4.

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http://dx.doi.org/10.1002/pro.285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817842PMC
January 2010

Mechanistic investigations of horseradish peroxidase-catalyzed degradation of single-walled carbon nanotubes.

J Am Chem Soc 2009 Dec;131(47):17194-205

Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

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http://dx.doi.org/10.1021/ja9083623DOI Listing
December 2009

Alternative paths in HIV-1 targeted human signal transduction pathways.

BMC Genomics 2009 Dec 3;10 Suppl 3:S30. Epub 2009 Dec 3.

Language Technologies Institute, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1186/1471-2164-10-S3-S30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788384PMC
December 2009

Heterolytic reduction of fatty acid hydroperoxides by cytochrome c/cardiolipin complexes: antioxidant function in mitochondria.

J Am Chem Soc 2009 Aug;131(32):11288-9

Center for Free Radical and Antioxidant Health and Department of Environmental and Occupational Health, University of Pittsburgh, 100 Technology Drive, Suite 350, Pittsburgh, Pennsylvania 15219-3130, USA.

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http://pubs.acs.org/doi/abs/10.1021/ja904343c
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http://dx.doi.org/10.1021/ja904343cDOI Listing
August 2009

pH-dependent interaction of rhodopsin with cyanidin-3-glucoside. 1. Structural aspects.

Photochem Photobiol 2009 Mar-Apr;85(2):454-62. Epub 2009 Jan 19.

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1111/j.1751-1097.2008.00517.xDOI Listing
July 2009

pH-dependent interaction of rhodopsin with cyanidin-3-glucoside. 2. Functional aspects.

Photochem Photobiol 2009 Mar-Apr;85(2):463-70

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1111/j.1751-1097.2008.00533.xDOI Listing
July 2009

Additive effects of chlorin e6 and metal ion binding on the thermal stability of rhodopsin in vitro.

Photochem Photobiol 2009 Mar-Apr;85(2):471-8

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1111/j.1751-1097.2009.00539.xDOI Listing
July 2009

Prediction of interactions between HIV-1 and human proteins by information integration.

Pac Symp Biocomput 2009 :516-27

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3263379PMC
March 2009

The effect of loops on the structural organization of alpha-helical membrane proteins.

Biophys J 2009 Mar;96(6):2299-312

Language Technologies Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.1016/j.bpj.2008.12.3894DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717299PMC
March 2009

Protein complex identification by supervised graph local clustering.

Bioinformatics 2008 Jul;24(13):i250-8

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718642PMC
July 2008

A mixture of feature experts approach for protein-protein interaction prediction.

BMC Bioinformatics 2007 ;8 Suppl 10:S6

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-8-S10-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2230507PMC
April 2008

Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors.

BMC Bioinformatics 2008 ;9 Suppl 1:S16

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.

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http://dx.doi.org/10.1186/1471-2105-9-S1-S16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2259417PMC
April 2008

Isotope labeling of mammalian GPCRs in HEK293 cells and characterization of the C-terminus of bovine rhodopsin by high resolution liquid NMR spectroscopy.

J Biomol NMR 2008 Jan 13;40(1):49-53. Epub 2007 Nov 13.

Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, Frankfurt/Main, D-60438, Germany.

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http://dx.doi.org/10.1007/s10858-007-9205-3DOI Listing
January 2008

Comparison of stability predictions and simulated unfolding of rhodopsin structures.

Photochem Photobiol 2007 Mar-Apr;83(2):351-62

Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1562/2006-06-20-RA-942DOI Listing
October 2007

TMpro web server and web service: transmembrane helix prediction through amino acid property analysis.

Bioinformatics 2007 Oct 27;23(20):2795-6. Epub 2007 Aug 27.

Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3263380PMC
October 2007

Evolutionary insights from suffix array-based genome sequence analysis.

J Biosci 2007 Aug;32(5):871-81

Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India.

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August 2007

Combined solid state and solution NMR studies of alpha,epsilon-15N labeled bovine rhodopsin.

J Biomol NMR 2007 Apr 23;37(4):303-12. Epub 2007 Feb 23.

Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main, Germany.

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http://dx.doi.org/10.1007/s10858-007-9143-0DOI Listing
April 2007

Predisposition of the dark state of rhodopsin to functional changes in structure.

Proteins 2006 Dec;65(4):970-83

Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

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December 2006

Retinitis pigmentosa associated with rhodopsin mutations: Correlation between phenotypic variability and molecular effects.

Vision Res 2006 Dec 2;46(27):4556-67. Epub 2006 Oct 2.

Hamilton Eye Institute, Department of Ophthalmology, Retinal Degeneration and Ophthalmic Genetics Service, University of Tennessee Health Science Center, 930 Madison Avenue, Suit 731, Memphis, TN 38163, USA.

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http://dx.doi.org/10.1016/j.visres.2006.08.018DOI Listing
December 2006

Shape and oligomerization state of the cytoplasmic domain of the phototaxis transducer II from Natronobacterium pharaonis.

Proc Natl Acad Sci U S A 2006 Oct 10;103(42):15428-33. Epub 2006 Oct 10.

Institute for Structural Biology and Institute of Solid-State Research, Research Center Juelich, 52425 Juelich, Germany.

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http://dx.doi.org/10.1073/pnas.0607201103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1592645PMC
October 2006

Evaluation of different biological data and computational classification methods for use in protein interaction prediction.

Proteins 2006 May;63(3):490-500

School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

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http://dx.doi.org/10.1002/prot.20865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250929PMC
May 2006

Glutamic acid-rich proteins of rod photoreceptors are natively unfolded.

J Biol Chem 2006 Jan 9;281(3):1449-60. Epub 2005 Nov 9.

Institut für Biologische Informationsverarbeitung 1, Forschungszentrum Jülich, Germany.

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http://dx.doi.org/10.1074/jbc.M505012200DOI Listing
January 2006

A sequence alignment-independent method for protein classification.

Appl Bioinformatics 2004 ;3(2-3):137-48

Department of Molecular Genetics and Biochemistry, School of Medicine, Center for Computational Biology and Bioinformatics, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15213, USA.

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December 2005

Inferring property selection pressure from positional residue conservation.

Appl Bioinformatics 2004 ;3(2-3):167-79

School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.

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December 2005

BLMT: statistical sequence analysis using N-grams.

Appl Bioinformatics 2004 ;3(2-3):193-200

Language Technologies Institute, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.

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December 2005

Random forest similarity for protein-protein interaction prediction from multiple sources.

Pac Symp Biocomput 2005 :531-42

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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April 2005

Dual role of interactions between membranous and soluble portions of helical membrane receptors for folding and signaling.

Trends Pharmacol Sci 2005 Apr;26(4):183-9

Department of Pharmacology, University of Pittsburgh School of Medicine, Biomedical Science Tower E1058, 200 Lothrop St, Pittsburgh, PA 15261, USA.

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http://dx.doi.org/10.1016/j.tips.2005.02.009DOI Listing
April 2005

Protein classification based on text document classification techniques.

Proteins 2005 Mar;58(4):955-70

Language Technologies Institute, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania, USA.

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http://dx.doi.org/10.1002/prot.20373DOI Listing
March 2005

Comparison of probabilistic combination methods for protein secondary structure prediction.

Bioinformatics 2004 Nov 24;20(17):3099-107. Epub 2004 Jun 24.

Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA15213, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth370DOI Listing
November 2004

Modulation of compactness and long-range interactions of unfolded lysozyme by single point mutations.

Angew Chem Int Ed Engl 2004 Nov;43(43):5780-5

Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt, Marie-Curie-Strasse 11, 60439 Frankfurt, Germany.

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http://dx.doi.org/10.1002/anie.200460907DOI Listing
November 2004

The optimal fraction of hydrophobic residues required to ensure protein collapse.

J Mol Biol 2004 Nov;344(3):797-811

Carnegie Mellon University School of Computer Science, Language Technologies Institute, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1016/j.jmb.2004.09.061DOI Listing
November 2004

Identification of core amino acids stabilizing rhodopsin.

Proc Natl Acad Sci U S A 2004 May 3;101(19):7246-51. Epub 2004 May 3.

Center for Computational Biology and Bioinformatics, Department of Molecular Biology and Biochemistry, School of Medicine, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15261, USA.

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http://dx.doi.org/10.1073/pnas.0401429101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC409904PMC
May 2004

Differential dynamics in the G protein-coupled receptor rhodopsin revealed by solution NMR.

Proc Natl Acad Sci U S A 2004 Mar 27;101(10):3409-13. Epub 2004 Feb 27.

Department of Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.

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http://dx.doi.org/10.1073/pnas.0308713101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373475PMC
March 2004

Dynamics in rhodopsin.

Chembiochem 2002 Oct;3(10):981-6

Department of Pharmacology, University of Pittsburgh School of Medicine, E1355 Biomedical Science Tower, Pittsburgh, PA 15261, USA.

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http://dx.doi.org/10.1002/1439-7633(20021004)3:10<981::AID-CBIC981>3.0.CO;2-9DOI Listing
October 2002

Long-range interactions within a nonnative protein.

Science 2002 Mar;295(5560):1719-22

Massachusetts Institute of Technology, Department of Chemistry, Francis Bitter Magnet Laboratory, 170 Albany Street, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/science.1067680DOI Listing
March 2002